Variant report

Variant	rs2008537
Chromosome Location	chr12:50538625-50538626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50467353..50469226-chr12:50536812..50539286,2	MCF-7	breast:
2	chr12:50529914..50531795-chr12:50537950..50540041,2	K562	blood:
3	chr12:50525700..50528015-chr12:50536583..50539181,2	MCF-7	breast:
4	chr12:50478449..50481902-chr12:50536030..50539935,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139624	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10735822	0.90[EUR][1000 genomes]
rs10735823	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10747571	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783336	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783337	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10783339	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875999	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876001	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876002	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876004	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10876006	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876007	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169283	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169284	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169285	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12229758	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12314572	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17124448	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2242507	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2277355	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55639096	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56151073	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7131794	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297864	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7306213	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7314598	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7316344	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7486874	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7953174	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
2	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:50520200-50539000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
5	chr12:50524600-50541600	Weak transcription	Psoas Muscle	Psoas
6	chr12:50528800-50543000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:50529600-50542800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:50529800-50543000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:50529800-50559800	Weak transcription	NHLF	lung
10	chr12:50530000-50538800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:50530000-50539600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:50530000-50559600	Weak transcription	A549	lung
13	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
14	chr12:50531200-50548400	Weak transcription	HUVEC	blood vessel
15	chr12:50531600-50543200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:50531600-50558200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:50531800-50544600	Weak transcription	Fetal Kidney	kidney
18	chr12:50531800-50554400	Weak transcription	K562	blood
19	chr12:50531800-50558400	Weak transcription	Fetal Brain Male	brain
20	chr12:50532000-50539600	Weak transcription	Brain Substantia Nigra	brain
21	chr12:50532000-50560200	Weak transcription	Aorta	Aorta
22	chr12:50532000-50560200	Weak transcription	Gastric	stomach
23	chr12:50532400-50538800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:50532400-50538800	Weak transcription	Brain Anterior Caudate	brain
25	chr12:50532400-50541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:50532400-50541400	Weak transcription	Liver	Liver
27	chr12:50532400-50559800	Weak transcription	Spleen	Spleen
28	chr12:50532800-50542200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:50533200-50544800	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:50533200-50559400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:50533400-50551200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:50534400-50560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:50534600-50544800	Weak transcription	Ovary	ovary
34	chr12:50535000-50545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:50535200-50541800	Weak transcription	Lung	lung
36	chr12:50535200-50545000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:50535200-50560000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr12:50535200-50560200	Weak transcription	Right Ventricle	heart
39	chr12:50535400-50559400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:50535400-50560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:50536400-50560200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:50536800-50545000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:50537000-50539400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:50537000-50539800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:50537000-50544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:50537200-50539400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:50537200-50539600	Weak transcription	Fetal Intestine Large	intestine
48	chr12:50537200-50558200	Weak transcription	Fetal Brain Female	brain
49	chr12:50537200-50559200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:50537400-50538800	Strong transcription	Fetal Intestine Small	intestine

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